I've been using NETCDF compression since V3.5, when it first started. I have the variable set to NETCDF4=1. I use NETCDF version 4.4.1.1. When I run the configure script, I get :

NetCDF users note: This installation of NetCDF supports large file support. To DISABLE large file support in NetCDF, set the environment variable WRFIO_NCD_NO_LARGE_FILE_SUPPORT to 1 and run configure again. Set to any other value to avoid this message.

Testing for NetCDF, C and Fortran compiler

This installation of NetCDF is 64-bit C compiler is 64-bit Fortran compiler is 64-bit It will build in 64-bit

*****************************************************************************This build of WRF will use classic (non-compressed) NETCDF format*****************************************************************************

It then compiles just fine. (Intel compiler and Intel MPI).

nothing has changed in my setup from V3.9.1.1 to V4. Is there something I'm missing? Is it really going to use compression (just a false warning), or is there something else I have to do in V4?

I had the same issue. To get it to configure/compile with netcdf-4, I ended up modifying the configure script. The sections that check netcdf have changed from v3, and somewhere in there it was throwing back that I didn't have netcdf4 with hdf5 compression, even though I did.

I didn't trace the code to figure out exactly where the issue was, but I ended up just hard coding"export NETCDF4=1" and "unset NETCDF_classic" after the script tries to set it automatically.

I think I found the issue in configure. Around line 207 there is an if statement checking if the script should use "whereis nf-config" or "which nf-config" depending if the OS is Darwin or Linux. When I changed it so Linux systems use which, it configured with the correct settings (i.e., with compression).

At the end of the checks for netcdf 4 and before if [ -z "$HDF5_PATH" ] ; then HDF5_PATH=''; fi , which is around line 237 in config, I inserted:

export NETCDF4=1unset NETCDF_classic

If it fails to compile with those, then there might be something else going on. I updated all my several-year-old-libraries (hdf/netcdf/etc) before compiling WRFV4, so there might be something different there, too.

To check which if statement is throwing back something it shouldn't, I inserted a bunch of echo statements to see where the issue was. That might help track down what is going on with your environment.